dr. ir. B. (Bas) van Breukelen
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Bas van Breukelen joined the Science faculty March 2003. He received his PhD at the Utrecht Medical Centre in 2003 on the subject of the Adenovirus DNA replication and recombination. After his PhD he worked at the department of Biology where he developed a LIMS and pipeline for (statistical) analysis of microarray data.
In 2005 he switched positions to work at the department of Biomolecular Mass Spectrometry where he works staff member (UD) in the field of Bioinformatics for proteomics. Since 2014 He is also involved in the Utrecht Bioinformatics Center (UBC) http://ubc.uu.nl as coordinator and executive Committee member. 

Involved in the following study programme(s)
Scientific expertise
Gegenereerd op 2017-11-19 15:18:14
Curriculum vitae

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All publications
  2015 - Scholarly publications
Giansanti, Piero, Aye, Thin Thin, van den Toorn, Henk, Peng, Mao, van Breukelen, Bas & Heck, Albert J R (10.06.2015). An Augmented Multiple-Protease-Based Human Phosphopeptide Atlas. Cell Reports, 11 (11), (pp. 1834-1843) (10 p.). Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved..
Peng, Mao, Aye, Thin Thin, Snel, Berend, Van Breukelen, Bas, Scholten, Arjen & Heck, Albert J R (02.07.2015). Spatial Organization in Protein Kinase A Signaling Emerged at the Base of Animal Evolution. Journal of Proteome Research, 14 (7), (pp. 2976-2987) (12 p.).
  2014 - Scholarly publications
Guerreiro, Ana C L, Benevento, Marco, Lehmann, Robert, van Breukelen, Bas, Post, Harm, Giansanti, Piero, Altelaar, Adrianus, Axmann, Ilka M & Heck, Albert J R (2014). Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins. Molecular and Cellular Proteomics, 13 (8), (pp. 2042-2055) (14 p.). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc..
Liu, Fan, van Breukelen, Bas & Heck, Albert J R (2014). Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Molecular and Cellular Proteomics, 13 (10), (pp. 2776-86) (11 p.). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc..
Peng, Mao, Scholten, Arjen, Heck, Albert J R & van Breukelen, Bas (03.01.2014). Identification of Enriched PTM Crosstalk Motifs from Large-Scale Experimental Data Sets. Journal of Proteome Research, 13 (1), (pp. 249-259) (11 p.).
Binai, Nadine A, Bisschops, Markus M M, van Breukelen, Bas, Mohammed, Shabaz, Loeff, Luuk, Pronk, Jack T, Heck, Albert J R, Daran-Lapujade, Pascale & Slijper, Monique (01.08.2014). Proteome adaptation of Saccharomyces cerevisiae to severe calorie restriction in Retentostat cultures. Journal of Proteome Research, 13 (8), (pp. 3542-3553) (12 p.).
Walzer, Mathias, Pernas, Lucia Espona, Nasso, Sara, Bittremieux, Wout, Nahnsen, Sven, Kelchtermans, Pieter, Pichler, Peter, van den Toorn, Henk W P, Staes, An, Vandenbussche, Jonathan, Mazanek, Michael, Taus, Thomas, Scheltema, Richard A, Kelstrup, Christian D, Gatto, Laurent, van Breukelen, Bas, Aiche, Stephan, Valkenborg, Dirk, Laukens, Kris, Lilley, Kathryn S, Olsen, Jesper V, Heck, Albert J R, Mechtler, Karl, Aebersold, Ruedi, Gevaert, Kris, Vizcaíno, Juan Antonio, Hermjakob, Henning, Kohlbacher, Oliver & Martens, Lennart (2014). qcML - an exchange format for quality control metrics from mass spectrometry experiments. Molecular and Cellular Proteomics, 13 (8), (pp. 1905-13) (9 p.). © 2014 by The American Society for Biochemistry and Molecular Biology, Inc..
Smit, Marjon A, Maddalo, Gianluca, Greig, Kylie, Raaijmakers, Linsey M, Possik, Patricia A, van Breukelen, Bas, Cappadona, Salvatore, Heck, Albert Jr, Altelaar, Adrianus & Peeper, Daniel S (2014). ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Molecular Systems Biology, 10 (12), (pp. 772) (1 p.). © 2014 The Authors. Published under the terms of the CC BY 4.0 license..
  2013 - Scholarly publications
Low, T.Y., van Heesch, S.A.A.C., van den Toorn, H.W.P., Giansanti, P., Cristobal, A., Toonen, P., Schafer, S., Hübner, N., van Breukelen, B., Mohammed, S., Cuppen, E.P.J.G. & Heck, A.J.R. (2013). Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis. Cell Reports, 5 (5), (pp. 1469-1478) (10 p.). http://linkinghub.elsevier.com/retrieve/pii/S2211-1247(13)00640-2.
  2012 - Scholarly publications
Cappadona, S., Baker, P.R., Cutillas, P., Heck, A.J.R. & van Breukelen, B. (2012). Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids, 43, (pp. 1087-1108) (22 p.).
Altelaar, A.F.M., Navarro, D., Boekhorst, J., van Breukelen, B., Snel, B., Mohammed, S. & Heck, A.J.R. (2012). Database independent proteomics analysis of the ostrich and human proteome. Proceedings of the National Academy of Sciences of the United States of America, 109, (pp. 407-412) (6 p.).
Bleijerveld, O.B., Wijten, P., Cappadona, S., McClellan, E.A., Polat, A.N., Raijmakers, R., Sels, J.W., Colle, L.B., Grasso, S., van den Toorn, H.W.P., van Breukelen, B., Stubbs, A., Pasterkamp, G., Heck, A.J.R., Hoefer, I.E. & Scholten, A. (2012). Deep Proteome Profiling of Circulating Granulocytes Reveals Bactericidal/Permeability-Increasing Protein as a Biomarker for Severe Atherosclerotic Coronary Stenosis. Journal of Proteome Research, 11, (pp. 5235-5244) (10 p.).
Millioni, R., Tolin, S., Fadini, G.P., Falda, M., van Breukelen, B., Tessari, P. & Arrigoni, G. (2012). High confidence and sensitivity four-dimensional fractionation for human plasma proteome analysis. Amino Acids, 43 (2), (pp. 2199-2202) (4 p.).
Peng, M, Ms. Taouatas, N., Cappadona, S., van Breukelen, B., Mohammed, S., Scholten, A. & Heck, A.J.R. (2012). Protease bias in absolute protein quantitation. Nature Methods, 9 (6), (pp. 524-525) (2 p.).
Cote, R.G., Griss, J., Dianes, J.A., Wang, R., Wright, J.C., van den Toorn, H.W.P., van Breukelen, B., Heck, A.J.R., Hulstaert, N., Martens, L., Reisinger, F., Csordas, A., Ovelleiro, D., Perez-Rivevol, Y., Barsnes, H., Hermjakob, H. & Vizcaino, J.A. (2012). The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium. Molecular and Cellular Proteomics, 12, (pp. 1682-1689) (8 p.).
  2011 - Scholarly publications
Ahmad, I., Suits, F., Hoekman, B., Swertz, M.A., Byelas, H., Dijkstra, M., Hooft, R., Katsubo, D., van Breukelen, B., Bischoff, R. & Horvatovich, P. (2011). A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data. Bioinformatics, 27 (8), (pp. 1176-1178) (3 p.).
Cappadona, S., Munoz, J, Spee, W.P.E., Low, T.Y., Mohammed, S., van Breukelen, B. & Heck, A.J.R. (2011). Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides. Journal of Proteomics, 74 (10), (pp. 2204-2209) (6 p.).
Boekhorst, J., Boersema, P.J., Tops, B.B.J., van Breukelen, B., Heck, A.J.R. & Snel, B. (2011). Evaluating experimental bias and completeness in comparative phosphoproteomics analysis. PLoS One, 6 (8), (pp. 23276) (1 p.).
de Graaf, E.L., Altelaar, A.F.M., van Breukelen, B., Mohammed, S. & Heck, A.J.R. (2011). Improving SRM assay development: a global comparison between triple quadrupole, ion trap, and higher energy CID peptide fragmentation spectra. Journal of Proteome Research, 10 (9), (pp. 4334-4341) (8 p.).
van den Toorn, H.W.P., Munoz, J, Mohammed, S., Raijmakers, R., Heck, A.J.R. & van Breukelen, B. (2011). RockerBox: analysis and filtering of massive proteomics search results. Journal of Proteome Research, 10 (3), (pp. 1420-1424) (5 p.).
  2010 - Scholarly publications
Boersema, P.J., Foong, L.Y., Ding, V.M., Lemeer, S., van Breukelen, B., Philp, R., Boekhorst, J., Snel, B., den Hertog, J., Choo, A.B. & Heck, A.J. (2010). In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling. Molecular and Cellular Proteomics, 9 (1), (pp. 84-99) (16 p.).
van Breukelen, B., Georgiou, A., Drugan, M.M., Ms. Taouatas, N., Mohammed, S. & Heck, A.J.R. (2010). LysNDeNovo: an algorithm enabling de novo sequencing of Lys-N generated peptides fragmented by electron transfer dissociation. Rapid Communications in Mass Spectrometry, 10, (pp. 1196-1201) (6 p.).
Barbu, I.M., Smith, D.F., van Breukelen, B., van der Burgt, Y.E.M., Duursma, M.C., Heck, A.J.R., Heeren, R.M.A. & Krijgsveld, J. (2010). On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics. Rapid Communications in Mass Spectrometry, 24, (pp. 239-241) (3 p.).
Helbig, A.O., Rosati, S, Pijnappel, W.W.M., van Breukelen, B., Timmers, H.T.M., Mohammed, S., Slijper, M. & Heck, A.J.R. (2010). Perturbation of the yeast N-acetyltransferase NatB induces elevation of protein phosphorylation levels. BMC Genomics, 11, (pp. 685) (15 p.).
Helbig, A.O., Gauci, S., Raijmakers, R., van Breukelen, B., Slijper, M., Mohammed, S. & Heck, A.J.R. (2010). Profiling of N-acetylated protein termini provides in-depth insights into the N-terminal nature of the proteome. Molecular and Cellular Proteomics, 9, (pp. 928-939) (12 p.).
  2009 - Scholarly publications
van Breukelen, B., van den Toorn, H.W.P., Drugan, M.M. & Heck, A.J.R. (2009). StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry. BMC Bioinformatics (25), (pp. 1472-1473) (2 p.).
  2008 - Scholarly publications
Mohammed, S., Lorenzen, K., Kerkhoven, R., van Breukelen, B., Vannini, A., Cramer, P. & Heck, A.J.R. (2008). ) Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites. Analytical Chemistry, 80 (10), (pp. 3584-3592) (9 p.).
Gauci, S., van Breukelen, B., Lemeer, S.M., Krijgsveld, J. & Heck, A.J.R. (2008). A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing. Proteomics, 8 (23-24), (pp. 4898-4906) (9 p.). J EC.
Boekhorst, J., van Breukelen, B., Heck, A.J.R. & Snel, B. (2008). Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biology, 9, (pp. R144.1-R144.9) (9 p.).
Pinkse, M.W.H., Mohammed, S., Gouw, J.W., van Breukelen, B., Vos, H.R. & Heck, A.J.R. (2008). Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster. Journal of Proteome Research, 7, (pp. 687-697) (11 p.).
Lemeer, S.M., Pinkse, M.W.H., Mohammed, S., van Breukelen, B., den Hertog, J., Slijper, M. & Heck, A.J.R. (2008). Online automated in vivo zebrafish phosphoproteomics: From large-scale analysis down to a single embryo. Journal of Proteome Research, 7 (4), (pp. 1555-1564) (10 p.). J PR 1st International Immunonutrition Workshop.
  2007 - Scholarly publications
de Groot, M.J.L., Daran-Lapujade, P., van Breukelen, B., Knijnenburg, T.A., Hulster, E.A.F., Reinders, M.J.T., Pronk, J.T., Heck, A.J.R. & Slijper, M. (2007). Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology, 153, (pp. 3864-3878) (15 p.).
Dormeyer, W., Mohammed, S., van Breukelen, B., Krijgsveld, J. & Heck, A.J.R. (2007). Targeted Analysis of Protein Termini. Journal of Proteome Research
  2006 - Scholarly publications
Scholten, A., Poh, M.K., van Veen, A.A.B., van Breukelen, B., Vos, M.A. & Heck, A.J.R. (2006). Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP. Journal of Proteome Research, 5 (6), (pp. 1435-1447) (13 p.).
de Jong, H.M., van Breukelen, B., Wittink, R.A., Menke, F.L.H., Weisbeek, P.J. & van den Ackerveken, A.F.J.M. (2006). Membrane-associated transcripts in Arabidopsis; their isolation and characterisation by DNA microarray analysis and bioinformatics. Plant Journal, 46 (4), (pp. 708-721) (14 p.).
van Breukelen, B., Barendregt, A., Heck, A.J.R. & van den Heuvel, R.H.H. (2006). Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra. Rapid Communications in Mass Spectrometry, 20, (pp. 2490-2496) (7 p.).
  2004 - Scholarly publications
Stracker, T.H., Cassel, G.D., Ward, P., Loo, Y-M., van Breukelen, B., Carrington-Lawrence, S.D., Hamatake, R.K., van der Vliet, P.C., Weller, S.K., Melendy, T. & Weitzman, M.D. (2004). The Rep protein of Adeno-associated virus type 2 interacts with single-stranded DNA-binding proteins that enhance viral replication. Journal of Virology, 78 (1), (pp. 441-453) (13 p.).
  2000 - Scholarly publications
van Breukelen, B., Kanellopoulos, P.N., Tucker, P.A. & van der Vliet, P.C. (2000). The formation of a flexible DNA-binding protein chain is required for efficient DNA unwinding and adenovirus DNA chain elongation. Journal of Biological Chemistry, 275 (52), (pp. 40897-40903) (7 p.).
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Full name
dr. ir. B. van Breukelen Contact details
Hugo R. Kruytgebouw

Padualaan 8
Room O605
The Netherlands

Phone number (direct) +31 30 253 9761
Phone number (department) +31 30 253 5871
Postal address
Postbus 80.082
3508 TB    UTRECHT
The Netherlands
Mo Tue Wed Thu Fr

Would you like to have more information about me or the biomolecular mass spectrometry and proteomics group or the Utrecht Bioinformatics Center? Have a look at:

Biomoleculaire Mass Spectrometry and Proteomics

  • http://www.hecklab.com/
  • http://www.hecklab.com/person/bas-breukelen/

Utrecht Bioinformatics Center (UBC)

  • http://ubc.uu.nl/
Gegenereerd op 2017-11-19 15:18:14
Last updated 28.07.2015